1
|
Wang Y, Shah PT, Liu Y, Bahoussi AN, Xing L. Genetic Characteristics and Phylogeographic Dynamics of Echovirus. J Microbiol 2023; 61:865-877. [PMID: 37713068 DOI: 10.1007/s12275-023-00078-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 08/20/2023] [Accepted: 08/22/2023] [Indexed: 09/16/2023]
Abstract
Echoviruses belong to the genus Enterovirus in the Picornaviridae family, forming a large group of Enterovirus B (EV-B) within the Enteroviruses. Previously, Echoviruses were classified based on the coding sequence of VP1. In this study, we performed a reliable phylogenetic classification of 277 sequences isolated from 1992 to 2019 based on the full-length genomes of Echovirus. In this report, phylogenetic, phylogeographic, recombination, and amino acid variability landscape analyses were performed to reveal the evolutional characteristics of Echovirus worldwide. Echoviruses were clustered into nine major clades, e.g., G1-G9. Phylogeographic analysis showed that branches G2-G9 were linked to common strains, while the branch G1 was only linked to G5. In contrast, strains E12, E14, and E16 clustered separately from their G3 and G7 clades respectively, and became a separate branch. In addition, we identified a total of 93 recombination events, where most of the events occurred within the VP1-VP4 coding regions. Analysis of amino acid variation showed high variability in the a positions of VP2, VP1, and VP3. This study updates the phylogenetic and phylogeographic information of Echovirus and indicates that extensive recombination and significant amino acid variation in the capsid proteins drove the emergence of new strains.
Collapse
Affiliation(s)
- Yan Wang
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan, 030006, Shanxi, People's Republic of China
| | - Pir Tariq Shah
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan, 030006, Shanxi, People's Republic of China
| | - Yue Liu
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan, 030006, Shanxi, People's Republic of China
| | - Amina Nawal Bahoussi
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan, 030006, Shanxi, People's Republic of China
| | - Li Xing
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan, 030006, Shanxi, People's Republic of China.
- Shanxi Provincial Key Laboratory of Medical Molecular Cell Biology, Shanxi University, Taiyuan, 030006, People's Republic of China.
- Shanxi Provincial Key Laboratory for Prevention and Treatment of Major Infectious Diseases, Taiyuan, 030006, People's Republic of China.
- The Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, 030006, People's Republic of China.
| |
Collapse
|
2
|
Cheng W, Ji T, Zhou S, Shi Y, Jiang L, Zhang Y, Yan D, Yang Q, Song Y, Cai R, Xu W. Molecular epidemiological characteristics of echovirus 6 in mainland China: extensive circulation of genotype F from 2007 to 2018. Arch Virol 2021; 166:1305-1312. [PMID: 33638089 PMCID: PMC8036204 DOI: 10.1007/s00705-020-04934-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 11/04/2020] [Indexed: 11/26/2022]
Abstract
Echovirus 6 (E6) is associated with various clinical diseases and is frequently detected in environmental sewage. Despite its high prevalence in humans and the environment, little is known about its molecular phylogeography in mainland China. In this study, 114 of 21,539 (0.53%) clinical specimens from hand, foot, and mouth disease (HFMD) cases collected between 2007 and 2018 were positive for E6. The complete VP1 sequences of 87 representative E6 strains, including 24 strains from this study, were used to investigate the evolutionary genetic characteristics and geographical spread of E6 strains. Phylogenetic analysis based on VP1 nucleotide sequence divergence showed that, globally, E6 strains can be grouped into six genotypes, designated A to F. Chinese E6 strains collected between 1988 and 2018 were found to belong to genotypes C, E, and F, with genotype F being predominant from 2007 to 2018. There was no significant difference in the geographical distribution of each genotype. The evolutionary rate of E6 was estimated to be 3.631 × 10-3 substitutions site-1 year-1 (95% highest posterior density [HPD]: 3.2406 × 10-3-4.031 × 10-3 substitutions site-1 year-1) by Bayesian MCMC analysis. The most recent common ancestor of the E6 genotypes was traced back to 1863, whereas their common ancestor in China was traced back to around 1962. A small genetic shift was detected in the Chinese E6 population size in 2009 according to Bayesian skyline analysis, which indicated that there might have been an epidemic around that year.
Collapse
Affiliation(s)
- Wenjun Cheng
- Medical School, Anhui University of Science and Technology, Huainan, 232001, Anhui, People's Republic of China
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Tianjiao Ji
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Shuaifeng Zhou
- Hunan Provincial Centers for Disease Control and Prevention, Changsha, People's Republic of China
| | - Yong Shi
- Jiangxi Provincial Centers for Disease Control and Prevention, Nanchang, People's Republic of China
| | - Lili Jiang
- Yunnan Provincial Centers for Disease Control and Prevention, Kunming, People's Republic of China
| | - Yong Zhang
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Dongmei Yan
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Qian Yang
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Yang Song
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Ru Cai
- Medical School, Anhui University of Science and Technology, Huainan, 232001, Anhui, People's Republic of China.
| | - Wenbo Xu
- Medical School, Anhui University of Science and Technology, Huainan, 232001, Anhui, People's Republic of China.
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China.
| |
Collapse
|
3
|
Toczylowski K, Wieczorek M, Bojkiewicz E, Wietlicka-Piszcz M, Gad B, Sulik A. Pediatric Enteroviral Central Nervous System Infections in Bialystok, Poland: Epidemiology, Viral Types, and Drivers of Seasonal Variation. Viruses 2020; 12:v12080893. [PMID: 32824117 PMCID: PMC7472221 DOI: 10.3390/v12080893] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/09/2020] [Accepted: 08/11/2020] [Indexed: 12/15/2022] Open
Abstract
Enteroviruses are common causes of infections of the central nervous system (CNS) that in temperate climates tend to peak in the summer. The aim of the study was to describe epidemiology, drivers of seasonality, and types of enteroviruses causing infections of the CNS in children in Northeastern Poland. We prospectively collected data on children hospitalized with infection of the CNS attributed to enteroviruses in Bialystok, Poland, from January 2015 to December 2019. In total, 224 children were included. Nineteen different enterovirus types were identified in isolates collected from 188 children. Coxsackie B5 (32%), echovirus 30 (20%), and echovirus 6 (14%) were the three most common types. Enteroviruses were more prevalent during the summer–fall season. Infections caused by echovirus 30 peaked early in June and coxsackievirus B5 in July, whereas echovirus 6 peaked late in October. Phylogenetic analyses of these three enterovirus types showed multiple lineages co-circulating in this region. Mean air temperatures and precipitation rates were independently associated with monthly number of cases. Considering lack of effective treatment or vaccine, easy transmission of enteroviruses between susceptible individuals, their high mutation rate and prolonged time of viral shedding, continued monitoring and surveillance are imperative to recognize enteroviral infections of the CNS and the changes in circulation of enteroviruses in Poland.
Collapse
Affiliation(s)
- Kacper Toczylowski
- Department of Pediatric Infectious Diseases, Medical University of Bialystok, Waszyngtona 17, 15-274 Bialystok, Poland; (E.B.); (A.S.)
- Correspondence: ; Tel.: +48-857-450-680
| | - Magdalena Wieczorek
- Department of Virology, National Institute of Public Health—National Institute of Hygiene, Chocimska 24, 00-791 Warsaw, Poland; (M.W.); (B.G.)
| | - Ewa Bojkiewicz
- Department of Pediatric Infectious Diseases, Medical University of Bialystok, Waszyngtona 17, 15-274 Bialystok, Poland; (E.B.); (A.S.)
| | - Magdalena Wietlicka-Piszcz
- Department of Theoretical Foundations of Biomedical Sciences and Medical Computer Science, Nicolaus Copernicus University in Torun, L. Rydygier Collegium Medicum in Bydgoszcz, 9 M. Skłodowska-Curie St., 85-094 Bydgoszcz, Poland;
| | - Beata Gad
- Department of Virology, National Institute of Public Health—National Institute of Hygiene, Chocimska 24, 00-791 Warsaw, Poland; (M.W.); (B.G.)
| | - Artur Sulik
- Department of Pediatric Infectious Diseases, Medical University of Bialystok, Waszyngtona 17, 15-274 Bialystok, Poland; (E.B.); (A.S.)
| |
Collapse
|
4
|
Monge S, Benschop K, Soetens L, Pijnacker R, Hahné S, Wallinga J, Duizer E. Echovirus type 6 transmission clusters and the role of environmental surveillance in early warning, the Netherlands, 2007 to 2016. ACTA ACUST UNITED AC 2019; 23. [PMID: 30424830 PMCID: PMC6234528 DOI: 10.2807/1560-7917.es.2018.23.45.1800288] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Background In the Netherlands, echovirus type 6 (E6) is identified through clinical and environmental enterovirus surveillance (CEVS and EEVS). Aim We aimed to identify E6 transmission clusters and to assess the role of EEVS in surveillance and early warning of E6. Methods We included all E6 strains from CEVS and EEVS from 2007 through 2016. CEVS samples were from patients with enterovirus illness. EEVS samples came from sewage water at pre-specified sampling points. E6 strains were defined by partial VP1 sequence, month and 4-digit postcode. Phylogenetic E6 clusters were detected using pairwise genetic distances. We identified transmission clusters using a combined pairwise distance in time, place and phylogeny dimensions. Results E6 was identified in 157 of 3,506 CEVS clinical episodes and 92 of 1,067 EEVS samples. Increased E6 circulation was observed in 2009 and from 2014 onwards. Eight phylogenetic clusters were identified; five included both CEVS and EEVS strains. Among these, identification in EEVS did not consistently precede CEVS. One phylogenetic cluster was dominant until 2014, but genetic diversity increased thereafter. Of 14 identified transmission clusters, six included both EEVS and CEVS; in two of them, EEVS identification preceded CEVS identification. Transmission clusters were consistent with phylogenetic clusters, and with previous outbreak reports. Conclusion Algorithms using combined time–place–phylogeny data allowed identification of clusters not detected by any of these variables alone. EEVS identified strains circulating in the population, but EEVS samples did not systematically precede clinical case surveillance, limiting EEVS usefulness for early warning in a context where E6 is endemic.
Collapse
Affiliation(s)
- Susana Monge
- European Programme for Intervention Epidemiology Training (EPIET), European Centre for Disease Prevention and Control, (ECDC), Stockholm, Sweden.,Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Kimberley Benschop
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Loes Soetens
- Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands.,Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Roan Pijnacker
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Susan Hahné
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Jacco Wallinga
- Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands.,Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Erwin Duizer
- Centre for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| |
Collapse
|
5
|
Lizasoain A, Burlandy FM, Victoria M, Tort LFL, da Silva EE, Colina R. An Environmental Surveillance in Uruguay Reveals the Presence of Highly Divergent Types of Human Enterovirus Species C and a High Frequency of Species A and B Types. FOOD AND ENVIRONMENTAL VIROLOGY 2018; 10:343-352. [PMID: 29907902 DOI: 10.1007/s12560-018-9351-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 06/12/2018] [Indexed: 06/08/2023]
Abstract
Information about Human Enterovirus circulation in Uruguay is scarce. The aim of this study was to generate the first description about their circulation in the country through the study of sewage samples collected before and after the switch from Oral Poliovirus Vaccine to Inactivated Poliovirus Vaccine. Viruses were concentrated by an adsorption-elution to a negatively charged membrane, and real-time quantitative PCR and qualitative PCR methods were used to detect, quantify, and characterize enteroviruses. Positive samples were inoculated in RD cells and two passages were performed. Additionally, RD+ samples were subsequently passed onto L20B cells. Human Enteroviruses were detected in 67.6% of the samples, with concentrations between 4.9 and 6.6 Log10 genomic copies per liter. 10% of positive samples replicated in RD cells, of which none in L20B cells. Molecular characterization of Human Enterovirus strains directly detected from sewage sample concentrates allowed the identification of highly divergent members of species C such as Enterovirus C99 and Coxsackievirus A13, as well as the frequent detection of species A and B members (particularly Coxsackievirus A16 and Echovirus 6, respectively). Other detected types were Coxsackievirus A2, A22, B1, B5, Echovirus 5, and 9. The characterization of viruses isolated in cell culture revealed the presence of Echovirus 6 and Coxsackievirus B3. Despite the absence of poliovirus, a wide circulation of different enterovirus types was evidenced in Uruguayan sewage samples, highlighting that the local populations are exposed to different kinds of diseases originated by several human enterovirus.
Collapse
Affiliation(s)
- Andrés Lizasoain
- Laboratorio de Virología Molecular, CENUR Litoral Norte, Sede Salto, Universidad de la República, Gral. Rivera 1350, 50000, Salto, Uruguay
| | - Fernanda M Burlandy
- Laboratório de Enterovírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Avda. Brasil 4365, Rio de Janeiro, 21040-360, Brazil
| | - Matías Victoria
- Laboratorio de Virología Molecular, CENUR Litoral Norte, Sede Salto, Universidad de la República, Gral. Rivera 1350, 50000, Salto, Uruguay
| | - Luis F López Tort
- Laboratorio de Virología Molecular, CENUR Litoral Norte, Sede Salto, Universidad de la República, Gral. Rivera 1350, 50000, Salto, Uruguay
| | - Edson E da Silva
- Laboratório de Enterovírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Avda. Brasil 4365, Rio de Janeiro, 21040-360, Brazil
| | - Rodney Colina
- Laboratorio de Virología Molecular, CENUR Litoral Norte, Sede Salto, Universidad de la República, Gral. Rivera 1350, 50000, Salto, Uruguay.
| |
Collapse
|